This article was originally published by GlobalPost as part of "A New Inquisition," a special report produced in collaboration with the Pulitzer Center and the National Catholic Reporter. It was also featured in the National Catholic Reporter.

VATICAN CITY — Sister Pat Farrell and three other nuns crossed St. Peter’s Square through the fabled white columns, paused for a security check and entered the rust-colored Palace of the Holy Office.

It was April 18, 2012, and on entering the palazzo, they were aware of its history, that in this same building nearly 400 years earlier Galileo had been condemned as a heretic by the Roman Inquisition for arguing that the earth orbits around the sun.

Today, the palazzo houses the Congregation for the Doctrine of the Faith (CDF), the Vatican office that enforces adherence to church teaching. As president of Leadership Conference of Women Religious (LCWR), Sister Farrell and her executive colleagues had an appointment with the prefect, Cardinal William Levada, about a CDF investigation of their group by the forces that control the Vatican, who viewed the nuns as somehow going "off the reservation."

They were walking into what Hans Küng, the internationally renowned theologian who had his own battles in the palazzo, calls “a new Inquisition.”

On the 50th anniversary of the reform-driven Second Vatican Council, the nuns were accused of undermining church moral teaching by promoting “radical, feminist themes incompatible with the Catholic faith.” To many nuns, the CDF action is a turn toward the past, causing a climate of fear and a chill wind reaching into the lives of missionary leaders.

The Vatican wants control of the LCWR, an association of 1,500 superiors, representing 80 percent of American nuns. Most of the sisters, long active in the front lines of social justice, dispensed with their black habits and traditional jobs, like teaching school, after Vatican II.

The sisters are in a standoff with the male hierarchy under Pope Benedict XVI. But many leading cardinals and bishops have disgraced themselves by recycling pedophiles in the worst crisis for the church since the Protestant Reformation.

The main leadership council of American nuns embraced the Vatican II social justice gospel that has taken sisters to some of the poorest corners of the world to work with politically oppressed people, particularly in Latin America. But a stark drama of attrition has unfolded as the Vatican II generation reaches an eclipse. Since 1965, the number of American nuns has dropped by more than two-thirds, from 181,241 to 54,000 today.

In contrast, the rate of women joining religious orders has surged in Korea, South Vietnam, sub-Saharan Africa and parts of the Caribbean. Nowhere has the increase been more pronounced than in India. Five of the 10 largest religious institutes of women have headquarters in India, where only 1.6 percent of the population is Catholic.

“While India has nearly 50 million fewer Catholics than the United States does, it has over 30,000 more women religious,” wrote Jeff Ziegler in Catholic World Report.

The Vatican crackdown of LCWR has exposed a schizophrenic church. Interviews with missionary sisters in Rome, from India and other countries, register a deep fault line between cardinals immune from punishment, and nuns who work in poor regions with some of the world’s most beleaguered people. Religious sisters from other parts of the world view the LCWR’s conflict with foreboding. How far Benedict goes in imposing a disciplinary culture, policing obedience over nuns as they push a Vatican II gospel of social justice, is an urgent issue to many of these women — and one sure to color this pope’s place in history.

The Doctrinal Assessment delivered by Levada was an intervention plan on how the nuns should pray; he appointed Archbishop Peter Sartain of Seattle to approve speakers for LCWR gatherings. The Vatican also signaled a striking interest in nuns’ property amid financial convulsions that have seen many American bishops sell churches to stanch deficits.

“You can impose silence, but that doesn’t change anyone’s thinking,” Sister Farrell reflected, several months later at the Franciscan convent in Dubuque, Iowa, where she lives.

“This is about the Vatican II church, how we have come to live collegially with participatory decision-making,” Farrell explains. “When I entered in 1965 we studied and prayed with [the Vatican II] documents, implementing new charters. ... We’re in a line of continuity with the early history of our communities, assessing unmet needs, going to the margins to help the homeless, people with AIDS, victims of torture and sexual trafficking.”

“When Vatican II requested nuns to search their history, Rome believed in a mythology of plaster statue women,” says Syracuse University Professor Margaret Susan Thompson, a historian of women religious. “They found instead nuns who took the job literally, and became controversial for doing so.”

The leadership conference endorsed women’s ordination in 1977 — 12 years before Pope John Paul II officially banned it. Farrell says they have not campaigned for it. Nor has LCWR endorsed abortion. The CDF demand that the leaders speak out against abortion and gay rights is a battle over conscience, forcing words into superiors’ mouths. Seattle Archbishop Sartain, the CDF delegate to oversee the group, is tasked with approving their conference speakers, a hotly contentious issue.

"These women are really rooted in Christ and committed to the poor,” says Sister Nzenzili Lucie Mboma, executive director of Service of Documentation and Studies on Mission, in Rome. A Congolese, Sister Lucie had two friends murdered in political violence in the 1960s, during her novice years. “It is painful to see the Vatican carrying on these kinds of things,” she says.

“In certain parts of the church we have an us-versus-them mentality,” says Father Míceál O’Neill, an Irish Carmelite prior in Rome with background as a missionary in Peru.

“'Us' is religious, and 'them' is officers of the Holy See.”

“We have a church that is doctrinally conservative and pastorally liberal,” says O’Neill. “The Vatican is trying to assert control, ‘we are in charge’ … Many people are saying the two churches are not coming together.”

“There is a fundamental problem of honesty.”

Sister Farrell, 65, came of age in Iowa in the heady years of Vatican II. She joined the Franciscans at 18, and in her 30s worked with Mexicans in San Antonio. She moved to Chile in 1980 during the brutal dictatorship of Augusto Pinochet. Disappearances were common. “It was routine for police to torture people in the first 72 hours,” she says. Demonstrations were banned, yet protests were the only way to put a spotlight on abductions when lives were at stake.

She joined “lightning-demonstrations,” unfurling banners of the anti-torture protest movement in congested traffic, spreading leaflets that gave people information on the missing who were airbrushed out of news reports. At one point she was arrested, with 100 other people, but coverage in a growing clandestine media saw them released the same day.

In 1986 she moved to El Salvador with a handful of sisters to help people reeling from a grisly civil war with US military support of the government. In 1980 Archbishop Oscar Romero had been shot dead while saying Mass; several months later, three nuns and a laywoman from America working with the poor were kidnapped, raped and murdered.

Farrell spent her first weeks sleeping at night in a church sacristy, getting to know people, and eventually moving into a sprawling refugee camp. The bishop supported their mission, because she lived with villagers displaced by military bombings. American nuns were a nonviolent presence giving thin cover to locals. What she remembers most of those years is walking, miles and miles of walking with the people.

“We learned never to leave the road because any area off defined footpaths could have land mines,” she explains. “I remember walking down one long hill with trembling knees to meet a group of soldiers who entered the camp. Part of our role as internationals in the camp was to keep the military out and I was on my way down to ask them to leave. That time they did, thank God.”

Religious processions common to Latin America took on heightened meaning. For a newly repopulated community to show up en masse, with banners of saints and the Virgin Mary, conveyed “a political statement.” As she puts it, “we are not afraid. We have a right to be here. Our faith continues to be a source of strength to us.”

One woman who fled the death squads, moving at night, toting a baby from town to town, made it safely into Honduras — but the baby died. As the war wound down, the woman returned to El Salvador with aching spasms in the shoulder and chest. After training as a therapist, Farrell used a treatment model for torture victims, helping the woman unpack the pain embedded from guilt over the baby’s death.

In 2005 Farrell returned to the Dubuque convent of the Franciscan sisters that she had entered at 18. Elected to the LCWR board several years later, she was midway through her one-year term as president when they made their annual trip to Rome, in April, to update church officials on their work. With Farrell were Sisters Mary Hughes, the past LCWR president; president-elect Florence Deacon, and Janet Mock, the executive director.

Before their appointment in the Palace of the Holy Office, they held an hour of silent prayer in a Carmelite center.

The prefect, Cardinal Levada, was about to turn 76 and retire to his native California. Putting LCWR under investigation for “radical feminist themes” followed his view of how sacred truth, the teaching of the church, must be upheld.

Doctrinal truth is a tightly held process in the hands of the definer. Levada, like nearly every bishop or cardinal in the constellation of hierarchs involved with the LCWR investigation, had shown unbending tolerance as an archbishop in America toward priests who were sexual predators.

In 2005, the newly elected Benedict XVI lifted Archbisop Levada from the muck of victim lawsuits and bad press in San Francisco to the Holy Office in Rome. Levada is the only US bishop to be sued, successfully, for defamation by a priest he pulled from a parish for blowing the whistle on another priest. Father Jon Conley told police that the pastor with whom he served made advances on a teenage boy. Levada yanked Conley from ministry; Conley, a former US attorney, sued. After the accused priest owned up in a civil case, which paid the victim’s family $750,000, the archdiocese paid Conley a six-figure “pre-retirement” settlement.

The nuns had met once with the CDF investigator, Bishop Leonard Blair of Toledo, Ohio, but had not seen his report. Blair had left an accused pederast in a fundraising job for 18 months, removing him only as the diocese was paying off two victims’ lawsuits. He was not in the meeting with Levada that day.

The nuns were expecting some conclusion to Blair’s inquiry but had no indication about what it would entail. After a cordial greeting, Cardinal Levada read aloud an eight-page, single-spaced assessment that his office was just posting on the web. The assessment accused the nuns of “corporate dissent” on homosexuality and failure to speak out on abortion. The assessment also castigated LCWR for ties to Network, a Catholic activist group that supported Obamacare, and Resource Center for Religious Institutes, a group that gives religious orders canon law guidance on property issues.

Leaving the Holy Office, Farrell felt numb. “It was in the press before we had time to brief our members,” she recalls.

“The reaction of rank-and-file sisters was anger. Now there is a stage of deep sadness and concern for the climate in the church and the misrepresentation of religious life,” she says.

In a darkly ironic twist, the CDF had processed 3,000 cases of priests who have been laicized, or defrocked for abusing youngsters. Several hundred are reportedly pending.

Yet those procedures that Benedict, as Cardinal Joseph Ratzinger, put in place as CDF prefect in 2001 have a large loophole. The office that enforces moral truth and judges guilty priests has not judged bishops and cardinals whose negligence in recycling abusers caused the crisis.

A double standard embedded in church justice gives a de facto immunity for men of the hierarchy.

In the most glaring example, Cardinal Bernard Law, whose soft-glove treatment of pedophiles ignited the Boston scandal, resigned as archbishop in 2002. The Roman Curia welcomed him in 2004 as pastor of a great basilica, Santa Maria Maggiore, with a $10,000 per month salary and a highly influential role in choosing new American bishops.

Law was a driving force behind a preliminary investigation of all American religious orders of women, save for cloistered communities, according to several sources interviewed here, and a May 15 report by Robert Mickens, the respected Vatican correspondent for the British magazine, The Tablet. Law, who has not spoken to the media in a decade, refused an interview request. But Cardinal Franc Rodé, 78, the retired prefect of the congregation that oversees religious orders, in a wide-ranging interview at his residence in the Palace of the Holy Office, confirmed Law’s role, adding: “It was the American milieu in the Roman Curia that suggested it.”

The “visitation” of all but the cloistered communities was the initial phase. The CDF aggressive investigation of the main leadership group soon followed.

But the specter of cardinals and bishops who played loose with child molesters, targeting nuns for doctrinal disobedience, is unseemly to many.

“Some people say this is an attempt to divert attention from the abuse crisis, like politicians do,” a missionary nun from a Third World country with her order in Rome, said of the CDF investigation.

“We go to US churches to solicit contributions for our work,” she said, insisting that her name and order not be used. “We get dates from dioceses. That could be in question if a bishops sees us as threatening because of our support for LCWR.”

“The Vatican is trying to assert control, to say ‘we are in charge,’” she continued. “This envisions a different church from Vatican II. Many people are saying that the two churches are not coming together.”

LCWR has indeed pushed the envelope with conventions giving forums to theologians who questioned celibacy and the evolution of religious life, at a time when far fewer women enter American convents and most members are moving toward elder care. As liberal theologians clamor for change, the LCWR has collided with the doctrinal office over freedom of conscience, a core principle of Vatican II.

Cardinal Rodé, as prefect of Congregation for Institutes of Consecrated Life and Societies of Apostolic Life, ordered the 2009 “visitation” of American nun communities. He told Vatican Radio of his concern for “a certain secular mentality … in these religious families and perhaps also a certain ‘feminist’ spirit.”

Rodé was also prompted by a 2008 conference he attended on religious life at Stonehill College near Boston. Sister Elizabeth McDonough, a canon lawyer, accused LCWR of creating “global-feminist-operated business corporations” and “controlling all structures and resources.”

“I'm unaware of any such facts that would back up that claim. It sounds like a sweeping indictment of the direction many orders have taken which the hierarchy found offensive or disloyal, summed up in the ‘radical feminism’ catch phrase,” says Kenneth A. Briggs, author of "Double Crossed: Uncovering the Catholic Church’s Betrayal of American Nuns."

“Most orders were scrounging to come up with funds to support retired sisters, often selling off property that belonged to them to do so. It seems clear to me that the aim of the Stonehill meeting was to paint a picture of disobedience as a pretext for a crackdown,” Briggs says.

Rodé in an interview brushed off suggestions that the visitation was unfair. “Vatican II was reform, but not a revolution,” he insists.

Rodé requested $1.3 million from religious communities and bishops to cover travel and other expenses for the visitation, which he appointed Mother Clare Millea, superior general of Apostles of the Sacred Heart of Mary, to carry out.

The funding request raised eyebrows among many missionary orders.

“Why would you want to pay them to investigate you?” asks one of the missionary sisters in Rome.

The study by Mother Millea has not been made public; however, the CDF began its investigation of LCWR before the first one was done.

“Vatican II was the most important event that changed the Catholic Church,” says Sister Nzenzili Lucie Mboma.

“Jesus was a carpenter. He didn’t build cells, but windows to see every culture.”

Author

Jason Berry is an author and investigative journalist based in New Orleans. He has done extensive reporting on the crisis in the Catholic Church in many articles, an award-winning documentary, "Vows...